February 2021 ODK 1.2.26 release (amended)

Some hotfixes and a features added to v.1.2.26 release (all pertaining to ODK repo template, not the tools)

• Hotfixes:
  • The new mireot module technique was buggy and is therefore removed again. Sorry; we will try again next time. You can still use the custom option to implement mireot yourself!
  • A change in the way imports were processed introduced a very high memory footprint for large ontologies and slowed stuff down. If you do not have a lot of memory (and time!) available, you should use the following new flags: is_large and use_gzipped. is_large: TRUE introduces a special handling for the ontology that is faster and consumes less memory when creating an import. Using use_gzipped will try to download the ontology from its gzipped location. Make sure its actually there (we know its the case for chebi and pr at least)!

import_group:
  products: 
    - id: pr
      use_gzipped: TRUE
      is_large: TRUE
    - id: chebi
      use_gzipped: TRUE
      is_large: TRUE

• An irrelevant file (keeprelations.txt) was still generated even if needed when seeding a new repo.
• Module type STAR was accidentally hard coded default for slme. Now changed to BOT as it was.
• CI configs where not correctly copied by update routine. Now it does. Note for the changes to be picked up, you need to run sh run.sh make update_repo twice (once for updating the update script itself)!
• Geeky (but necessary) all phony make goals are now correctly declared as .PHONY.
• Some last minute features:
  • In new repos, the README.md is now generated with the correct, appropriate banners.
  • We now have a new feature, custom_makefile_header, that allows injecting a custom header into the Makefile. Most mortals wont need this, but this is how it goes:

custom_makefile_header: |
  ### Workflow
  #
  # Tasks to edit and release OMRSE.
  #
  # #### Edit
  #
  # 1. [Prepare release](prepare_release)
  # 2. [Refresh imports](all_imports)
  # 3. [Update repo to latest ODK](update_repo)

• all features and fixes here: #397

2020-11-18 November release (Hotfix)

updated v1.2.25 (18 November 2020)

• Updated ROBOT to new version 1.7.2, which includes some hotfixes for ROBOT report and update to whelk 1.0.4
• Fixed a bug (#376) that prevented certain things (like imports and pattern generation processes) to be printed when running the Makefile.

2020-11-06 (1.2.24) ODK Release

• Updated ROBOT to new version 1.7.1
• Added the (highly experimental) ability to ODK to run OBO dashboard (see instructions and examples).
• Added more python packages to ODK, see requirements.txt.
• Added a new set of configurations for ROBOT report. WARNING:
  report_fail_on option is now deprecated in favour of a new block of options:

robot_report:
  use_labels: TRUE
  fail_on: None
  custom_profile: TRUE
  report_on:
    - .owl
    - .obo
    - edit

• use_labels: allows switching labels on and off in the ROBOT report, see here
• fail_on: is the old report_fail_on option, see here.
• custom_profile: allows switching on custom profiles, see here
• report_on allows specifying which files to run the report over (for example hp.owl, hp.obo, hp-edit.owl).

2020-08-06 (1.2.23) ODK Release

Changes:

• New ROBOT (v 1.7.0)
• New owltools (v. 2020-04-06)
• Added SWI Prolog and C. Mungall's sparqlprog tools
• Release artefacts are now annotated with owl:versionInfo
• run.sh now got the JAVA_OPTS parameter which is necessary to set the maximum memory allowed for owltools
• Bug fixes:
  • base-modules are now correctly annotated with resource references rather than strings (issue)
  • The ODK_VERSION variable in the Makefile was misnamed, which causes a circularity with updating it correctly when the Makefile is updated with a new ODK. This is fixed, but for the fix to kick in, you have to run sh run.sh make update_repo twice this time!

Please get the latest ODK from dockerhub.

2020-08-06 (1.2.23) ODK Release (UPDATED)

Changes:

Original changes:

• New ROBOT (v 1.7.0)
• New owltools (v. 2020-04-06)
• Added SWI Prolog and C. Mungall's sparqlprog tools
• Release artefacts are now annotated with owl:versionInfo
• run.sh now got the JAVA_OPTS parameter which is necessary to set the maximum memory allowed for owltools
• Bug fixes:
  • base-modules are now correctly annotated with resource references rather than strings (issue)
  • The ODK_VERSION variable in the Makefile was misnamed, which causes a circularity with updating it correctly when the Makefile is updated with a new ODK. This is fixed, but for the fix to kick in, you have to run sh run.sh make update_repo twice this time!

Please get the latest ODK from dockerhub.

Updated version:

• Added new version of fastobo (v0.3.0)
• Added rdflib to Python environment
• Added xlsx2csv command line tool

2020-03-06 (1.2.22) ODK Release

• New ROBOT (v. 1.6.0)
• Bugfixes:
  • Small fixes to update_repo method
  • the sparql query for extracting labeled subsets is now fixed
  • Some unneeded files (ontologyterms.txt) are removed from the default template.
  • a few more files are added to the .gitignore file
  • The catalog file is restructured to preclude Protege from changing it in unwanted ways.
  • the license in the ontology metadata is now required to be an IRI rather than a string.
  • The odk.py should now be executable in a non-docker context
  • JSON versions of imports are not anymore generated. OBO versions are only generated if OBO is used as the edit file serialisation.
  • PAT=false now skips pattern download
• Fixes to DOSDP pipeline
  • DOSDP tools is updated to version 0.14. This version comes with some great changes, including:
    • a mode in which multiple patterns can be compiled at once (batch mode)
    • we finally have have optional columns and column values!
  • external.txt can now be empty
  • instead of abnormalAnatomicalEntity, an example.yaml is added to the default pattern directory
• Infrastructure (only relevant to ODK developers):
  • The test framework for ODK is now more dynamic:
    1. Travis now correctly builds the ODK from scratch and runs the tests against the new build version
    2. Instead of adding new tests to the Makefile, you can simply now drop a new YAML file into the tests/ directory.
  • ODK Dockerfile has been optimised a bit for size (avoiding superfluous chmod calls)
  • the yaml loader in the ODK is now replaced by a safe loader

2020-01-23 Release (v. 1.2.21)

https://hub.docker.com/r/obolibrary/odkfull/tags?page=1&ordering=last_updated

• Changed base image of docker file
• added Ammonite to ODK

1.1.4 release

Added a .bat wrapper for windows users

1.1.3 release

Changes

• fixing bug in which running seed-via-docker did not enter interactive mode when no arguments provided
• added convenience wrapper scripts

Migration guide

• New .sh scripts in src/ontology can be directly copied across

1.1.2 release

Changes

• added interactive mode
• added DOSDP support

Docker

• odkfull v1.1.2 includes robot 1.1.0

Migration guide

This release adds a new template in the src/patterns folder. These can be copied across to an existing repo.